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- PDB-4gw4: Crystal structure of 3BNC60 Fab with P61A mutation -

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Basic information

Entry
Database: PDB / ID: 4gw4
TitleCrystal structure of 3BNC60 Fab with P61A mutation
Components
  • 3BNC60 Fab Heavy-chain
  • 3BNC60 Fab Light-chain
KeywordsIMMUNE SYSTEM / FWR / IgG / Anti HIV / gp120 / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDiskin, R. / Fu, B.Z. / Bjorkman, P.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization.
Authors: Klein, F. / Diskin, R. / Scheid, J.F. / Gaebler, C. / Mouquet, H. / Georgiev, I.S. / Pancera, M. / Zhou, T. / Incesu, R.B. / Fu, B.Z. / Gnanapragasam, P.N. / Oliveira, T.Y. / Seaman, M.S. / ...Authors: Klein, F. / Diskin, R. / Scheid, J.F. / Gaebler, C. / Mouquet, H. / Georgiev, I.S. / Pancera, M. / Zhou, T. / Incesu, R.B. / Fu, B.Z. / Gnanapragasam, P.N. / Oliveira, T.Y. / Seaman, M.S. / Kwong, P.D. / Bjorkman, P.J. / Nussenzweig, M.C.
History
DepositionAug 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 3BNC60 Fab Light-chain
H: 3BNC60 Fab Heavy-chain
A: 3BNC60 Fab Heavy-chain
B: 3BNC60 Fab Light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3256
Polymers95,8834
Non-polymers4422
Water3,585199
1
L: 3BNC60 Fab Light-chain
H: 3BNC60 Fab Heavy-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1633
Polymers47,9412
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-14 kcal/mol
Surface area19700 Å2
MethodPISA
2
A: 3BNC60 Fab Heavy-chain
B: 3BNC60 Fab Light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1633
Polymers47,9412
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-14 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.570, 154.880, 74.240
Angle α, β, γ (deg.)90.00, 109.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 3BNC60 Fab Light-chain


Mass: 23076.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Antibody 3BNC60 Fab Heavy-chain


Mass: 24864.656 Da / Num. of mol.: 2 / Mutation: P61A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.9
Details: 16% polyethylene glycol 6,000, 0.1 M citric acid pH 3.9, 0.15 M lithium sulfate monohydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→39.35 Å / Num. all: 39926 / Num. obs: 39093 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.65→2.72 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_966)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→39.346 Å / SU ML: 0.54 / σ(F): 1.35 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1954 5 %
Rwork0.2132 --
obs0.2154 39058 98.1 %
all-39926 -
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.874 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.9555 Å2-0 Å25.8892 Å2
2---4.4106 Å20 Å2
3----8.5449 Å2
Refinement stepCycle: LAST / Resolution: 2.65→39.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6400 0 28 199 6627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016603
X-RAY DIFFRACTIONf_angle_d1.3568984
X-RAY DIFFRACTIONf_dihedral_angle_d14.9172352
X-RAY DIFFRACTIONf_chiral_restr0.073992
X-RAY DIFFRACTIONf_plane_restr0.0081152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6499-2.71620.57061370.54492591X-RAY DIFFRACTION97
2.7162-2.78960.49751380.47122630X-RAY DIFFRACTION97
2.7896-2.87170.48831390.39832652X-RAY DIFFRACTION98
2.8717-2.96430.3161410.31042652X-RAY DIFFRACTION98
2.9643-3.07020.31051390.24052664X-RAY DIFFRACTION98
3.0702-3.19310.26311390.20932630X-RAY DIFFRACTION99
3.1931-3.33840.24521400.21532674X-RAY DIFFRACTION99
3.3384-3.51430.27931410.21382673X-RAY DIFFRACTION99
3.5143-3.73430.23891370.19962589X-RAY DIFFRACTION96
3.7343-4.02230.22591410.18482687X-RAY DIFFRACTION99
4.0223-4.42660.20731410.15492666X-RAY DIFFRACTION99
4.4266-5.0660.16511410.13952680X-RAY DIFFRACTION99
5.066-6.37830.22431380.18762641X-RAY DIFFRACTION97
6.3783-39.35050.26011420.21722675X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1516-0.6303-0.15762.69210.6820.17340.1256-0.49560.09040.60080.28221.18470.3611-1.5971-0.23630.5064-0.1470.08550.92460.0670.3428-33.382243.282-27.9162
27.913-0.35770.36373.6811.40847.1617-0.43210.0965-0.03-0.19130.4802-0.0135-0.3486-0.4256-0.03370.2165-0.0193-0.00450.29740.0390.2116-24.286550.168-18.6584
36.59442.9464-4.20373.19640.06914.7356-0.3528-0.32871.29980.97970.29451.0366-0.1096-1.1709-0.12360.54370.20420.11650.6927-0.01990.45-34.197254.4468-19.1818
40.56920.00950.78430.7613-0.91816.84820.2833-0.1124-0.2629-0.05290.19850.06470.85440.13750.67870.19590.04060.04640.43360.07040.2088-27.439242.7749-25.32
50.329-0.19440.31020.0868-0.20370.32150.19630.0858-1.0341-0.96670.27071.36511.092-0.0168-0.20391.2557-0.01250.03710.36020.09280.8336-25.466414.7863-33.2121
68.12635.3375-0.335.6995-1.71661.04580.01980.4001-1.9913-0.66730.82650.75811.4967-0.3439-0.01671.5683-0.06070.05550.44820.09761.3549-32.570311.5692-26.4521
73.01360.19970.92333.08441.19591.15220.3743-0.4528-0.83810.57610.4122-0.20030.49550.50070.79710.72970.04540.23650.34290.0740.3311-24.28617.5702-31.2915
80.98151.1458-0.96742.3108-0.26771.66680.10770.1082-0.8308-0.50060.42290.23280.9033-0.26281.09221.0455-0.2922-0.40090.44150.16891.6992-35.15715.5665-37.5939
94.0228-1.49810.52864.0861-0.11295.20170.0475-0.1493-0.56970.19180.0276-0.53240.21360.43650.03990.137-0.0034-0.01340.3422-0.01980.3673-13.14939.5344-3.6118
101.6399-1.66730.53843.898-0.89713.53720.1403-0.2317-0.1816-0.20860.0692-0.6842-0.07170.9020.20060.18570.0303-0.0220.4798-0.04780.4059-12.123740.9639-6.3643
113.13610.06161.43544.8875-0.47051.6712-0.16330.42830.0451-0.1865-0.0126-1.94370.48940.8606-0.2331.30330.3730.18940.5480.01230.9374-11.272917.2708-31.4038
124.94580.4055-0.61182.92361.29862.8119-0.1083-0.13510.39330.10130.1657-0.2545-0.27180.28740.08490.2401-0.0064-0.08540.3653-0.02630.2582-8.0291-21.4906-18.7784
134.19752.3731.14396.94350.02853.8650.259-0.3781-0.311.1151-0.1093-1.4738-0.83720.1509-0.23441.0182-0.1125-0.01610.3993-0.10190.7705-23.8411.4512.812
140.270.7793-0.43524.0994-0.9140.80860.29151.37010.3498-0.75150.2210.4807-0.1502-1.03920.11650.35960.06090.04090.92510.15770.3212-38.7762-24.4303-14.1687
157.0047-0.9391-0.0123.5937-0.00853.5624-0.23030.06890.32480.02190.37810.205-0.3819-0.47440.22650.0868-0.0567-0.04440.30380.04380.1644-26.7304-27.9736-16.6729
162.1555-0.6314-1.99512.29361.20332.13260.0637-0.6006-0.8880.06590.30360.0025-0.06460.6986-0.33110.2351-0.0013-0.02560.4344-0.01220.5413-24.1433-38.345-13.2122
172.0492-1.0348-1.69347.7766-3.99954.65630.15530.975-0.7546-1.49620.4060.67290.3637-0.82220.74510.3919-0.05730.01160.675-0.14150.3114-33.8804-35.5603-21.6196
183.9937-0.6245-3.94390.57060.97494.11570.25450.10960.555-0.18610.20380.029-0.38540.2137-0.12380.2101-0.0254-0.00380.43710.04470.1653-32.5162-23.8166-12.4845
192.05281.3494-0.31330.8785-0.25120.8261-0.19720.40351.4468-0.51220.41851.6352-0.7286-0.0903-0.10620.85710.015-0.01450.34860.13160.7562-35.76563.9218-5.0403
203.1233-2.62133.13122.1864-2.62463.1435-0.55260.35521.6923-0.26930.22630.2783-1.1167-0.2031-0.40221.4141-0.0301-0.04350.35640.18370.9708-36.62037.1316-14.7969
213.0661.7026-0.146.4957-0.25921.893-0.50380.03660.6799-0.60090.7211-0.2896-0.29910.45740.11290.62160.00140.01150.3045-0.01380.3785-33.60950.2714-5.3836
220.5475-0.5294-0.92890.52890.75792.52510.34920.40441.0804-0.33170.15420.3309-0.8155-0.313-0.05111.19660.0949-0.47450.6250.34521.9661-45.39824.8998-7.7759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 4 through 18 )
2X-RAY DIFFRACTION2chain 'L' and (resid 19 through 59 )
3X-RAY DIFFRACTION3chain 'L' and (resid 60 through 73 )
4X-RAY DIFFRACTION4chain 'L' and (resid 74 through 102 )
5X-RAY DIFFRACTION5chain 'L' and (resid 103 through 139 )
6X-RAY DIFFRACTION6chain 'L' and (resid 140 through 152 )
7X-RAY DIFFRACTION7chain 'L' and (resid 153 through 178 )
8X-RAY DIFFRACTION8chain 'L' and (resid 179 through 198 )
9X-RAY DIFFRACTION9chain 'H' and (resid 2 through 74 )
10X-RAY DIFFRACTION10chain 'H' and (resid 74a through 117 )
11X-RAY DIFFRACTION11chain 'H' and (resid 118 through 217 )
12X-RAY DIFFRACTION12chain 'A' and (resid 2 through 117 )
13X-RAY DIFFRACTION13chain 'A' and (resid 118 through 217 )
14X-RAY DIFFRACTION14chain 'B' and (resid 4 through 18 )
15X-RAY DIFFRACTION15chain 'B' and (resid 19 through 46 )
16X-RAY DIFFRACTION16chain 'B' and (resid 47 through 59 )
17X-RAY DIFFRACTION17chain 'B' and (resid 60 through 73 )
18X-RAY DIFFRACTION18chain 'B' and (resid 74 through 102 )
19X-RAY DIFFRACTION19chain 'B' and (resid 103 through 139 )
20X-RAY DIFFRACTION20chain 'B' and (resid 140 through 152 )
21X-RAY DIFFRACTION21chain 'B' and (resid 153 through 177 )
22X-RAY DIFFRACTION22chain 'B' and (resid 178 through 199 )

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